title: DO-140_F_Islet

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.


title: mock 1

status: Public on May 24 2024

type: SRA

city: Valencia

first: Vicente

last: Balanzà

state: Valencia

address: Av de los Naranjos s/n

department: Development and hormonal action

country: Spain

institute: IBMCP (CSIC-UPV)

library_source: transcriptomic

data_processing:
Paired-end sequencing (2 × 150 bp) was performed on a MiSeq (Illumina).
Reads were aligned to the reference genome of Arabidopsis thaliana available at the TAIR database (Lamesch et al., 2012) using TopHat (Trapnell et al., 2009) and Bowtie (Langmead et al., 2009) software.
The abundance estimation of the transcripts was performed using the RSEM package (Li and Dewey, 2011) and the differentially expressed transcripts (fragments per kilobase million value) were estimated using Cufflinks (Trapnell et al., 2010).
The sequences from DEG were annotated through BLAST search against the TAIR database
Assembly: Arabidopsis thaliana (TAIT10)
Supplementary files format and content: tab-delimited text file include tpm values for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Inflorescence meristem

growth_protocol: Plants were grown at 21°C under long day conditions (16 h light, 8h night), in a 2:1:1 by vol. mixture of peat:perlite:vermiculite.

extract_protocol:
RNA for RNA-seq was obtained with the RNeasy Plant Mini Kit (QUIAGEN)
The cDNA libraries were built using the Novogene Company United procedure for Illumina

treatment_protocol: Two weeks after bolting, inflorescence apexes of Arabidopsis 35S:LhG4:GR»HB21 (HB21 ind) plants were treated with dexamethasone, that allows the HB21 expression, or mock. 6-8 hours after treatment inflorescence apexes were collected removing all visible opened flowers.

tag: tissue

value: Inflorescence meristem

tag: genotype

tag: developmental stage

value: two weeks after bolting

tag: treatment

value: mock

tag: time

value: 6 hours post-treatment


title: SS-HDAC1

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

country: China

institute: westlake University

description: ChIP

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Assembly: hg38
Supplementary files format and content: bw

molecule: genomic DNA

organism: Homo sapiens

source_name: BJ

growth_protocol: fibroblasts were cultured by 10% FBS medium (DMEM, 10%FBS, NEAA, GlutaMAX)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions

treatment_protocol: overexpression by lentiviral infection.

tag: cell line

value: BJ

tag: cell type

value: fibroblasts

value: wild type

tag: antibody

value: SS18-SSX1 overexpression


title: Lane3_Sample_7

city: Columbus

first: Russell

last: Ault

state: OH

address: 370 W 9th Ave

country: USA

institute: The Ohio State University College of Medicine

data_processing:
Basecalls performed using bcl2fastq2 v.2.19
Adapter removal and quality trimming were performed by using Trim Galore! v.0.6.4
Alignment performed by BitMapperBS v.1.0.2.3 with default options: bitmapperBS --search ${REFERENCE} --seq1 ${R1} --seq2 ${R2} --bam -o Sample_${n}.bam
Methylation levels were determined using MethylDackel v.0.4.0 with default options: MethylDackel extract $DACKELREFERENCE $bam_file
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Processed files are MethylDackel bedGraph output files with 1. Chromosome name 2. Start coordinate 3. End coordinate 4. Methylation percentage 5. Number of alignments reporting methylated bases 6. Number of alignments reporting unmethylated bases

organism: Mus musculus

source_name: Whole Blood

extract_protocol:
Whole blood was collected, mixed with EDTA, and mixed with Zymo Research DNA/RNA Shield. DNA was isolated using the Zymo Research Quick-DNA kit and Genomic DNA Clean & Concentrator kit.
Libraries were prepared using Reduced Representation Bisulfite Sequencing. 52 samples were pooled together using custom synthesized methylated adapters with unique dual indexes (Integrated DNA Technologies).

value: Whole Blood

tag: mouse

tag: cage

value: infected

tag: strain

value: Balb/c

value: Heart


title: Group-IV A5V004 BUCCAL

type: RNA

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95243.gif

hyb_protocol: not provided

scan_protocol: scanner model: G2505C

data_processing: VALUE is Log RED/GREEN

organism: Macaca mulatta

source_name: 825 ng of amplified monkey POOLED Group I Buccal cDNA

label_protocol: not provided

extract_protocol: not provided

tag: tissue type

value: Oropharyngeal mucosal tissue

tag: infection

value: control

source_name: 825 ng of amplified monkey Group-IV A5V004 BUCCAL cDNA

value: LCV SIV

tag: individual


title: Lane3_Sample_5


title: DO-138_F_Islet

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Assembly: GRCm38
Supplementary files format and content: DO_RNAseq_islet_counts_matrix.csv
Supplementary files format and content: DO_RNAseq_islet_mrna_annots.csv
Supplementary files format and content: DO_RNAseq_islet_vst_matrix.csv
Islet: processed DO islet RNAseq data (legacy data, reprocessed with batch effects removed as reported in /RNAseq/Raw/GBRS/QTLViewer_setup/QTLv_format_ISLET_REMOVE_BATCH.R script).
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.
counts_matrix.csv: raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.
vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
mrna_annots.csv: gene annotation file ENSEMBL version 75.
QTLViewer: QTLViewer data object and documentation. QTLViewer object generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
GBRS_QTL2_genoprobs: final genoprobs on QTL2 format generated through GBRS for each tissue (used for genotype QCing). Genoprobs generated by the R script /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_genoprobs.R

source_name: pancreatic islet

treatment_protocol: Diversity Outbred mice were sensitized on a high-fat, high-sugar (HFHS) diet

value: pancreatic islet

tag: diet

value: 45% fat


title: Lane3_Sample_16


title: Group-IV 933 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95238.gif

source_name: 825 ng of amplified monkey Group-IV 933 BUCCAL cDNA


title: SS-IMR90-H2AK119ub

description: ChIP

source_name: IMR-90 cell line

value: IMR-90 cell line


title: DO-137_F_Islet


title: Lane3_Sample_1


title: SS-SUZ12

description: ChIP


title: Lane3_Sample_3

value: naive


title: mock 3

value: Inflorescence meristem

value: two weeks after bolting

value: mock


title: 26C_H3K27me3

city: cincinnati

first: XUEZHAO

last: LIU

institute: cincinnati children's hospital medical center

data_processing:
All sequencing data were mapped to rat genome rn5 and peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) version 1.4.2 (http://liulab.dfci.harvard.edu/MACS) with a P value cutoff of 1 x e-9 to obtain raw binding peaks
Assembly: rn5
Supplementary files format and content: wig,bigwig
Library strategy: Cut&Run

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Cut &Run cleaved fragments were purified by Qiagen MinElute PCR Purification Kit.
Libraries were prepared for Illumina sequencing with Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).

value: brain

value: primary iOLs

value: oligodendrocytes

value: wildtype


title: DO-133_F_Islet


title: Lane1_Sample_52

value: Whole Blood

value: infected


title: Lane3_Sample_4

value: Balb/c

value: Heart


title: Lane1_Sample_51


title: SS-RAD21

description: ChIP

value: BJ

value: fibroblasts

value: wild type

value: SS18-SSX1 overexpression


title: DO-131_F_Islet

value: pancreatic islet

value: 45% fat


title: DO-132_F_Islet


title: Lane1_Sample_50


title: SS-H3K27me3

description: ChIP


title: DO-130_F_Islet


title: Group-IV A5V037 BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95244.gif

value: Oropharyngeal mucosal tissue

value: control

source_name: 825 ng of amplified monkey Group-IV A5V037 BUCCAL cDNA

value: LCV SIV


title: DO-129_F_Islet


title: Lane1_Sample_48

value: naive


title: ChIPseq_DMC1_sticklebackTestesPool_Freshwater

city: Tuebingen

first: Felicity

middle: C

last: Jones

address: Max-Planck-Ring 9

country: Germany

institute: Friedrich Miescher Laboratory of the Max Planck Society

data_processing:
ChIPseq reads were trimmed to 40 bp using Trimmomatic (Bolger et al 2014 Bioinformatics 30:2114-20).
For DMC1 ChIP a specialized bioinformatic pipeline described in Khil et al (2012) Genome Research 22:957-65 was used to process paired-end sequencing data and extract 'Type 1' sequencing reads obtained from pulldown of DMC1-bound single stranded DNA.  This generated bedfiles used as input for MACS2 peak calling (described below).  This was not performed for H3K4me3 ChIPseq.
MACS2 (v2.1.1) was used to call peaks from DMC1 'Type 1' reads relative to DMC1 kinetic enrichment ChIP Input controls. (v2.1.1) with the following parameters: -q 0.1 --nomodel --slocal 5000 --llocal 10000 --extsize 800 -f BED --SPMR -g 463000000 -B. For H3K4me3 ChIP reads, macs2 peak calling was performed using default parameters.
ChIPseq normalized treatment coverage plots (DMC1 or H3K4me3 ChIP) and control (kinetic enrichment control, or H3K4me3 ChIPseq input control) coverage plots were generated using MACS2. narrowPeak files were generated using MACS2
Assembly: Broad/gasAcu1
Supplementary files format and content: bed (representing 'Type 1' DMC1-bound single stranded DNA reads used as input for MACS2; only for DMC1 ChIPseq), bedGraph (from MACS2 ChIPseq treatment and input controls), peak files (except for ChIP input samples)

organism: Gasterosteus aculeatus

source_name: TestesPool

growth_protocol: Wild-derived strains of marine and freshwater sticklebacks from the River Tyne, East Lothian, Scotland under a seasonally varying day length (3 months of 16 hours light, 8 hours dark, followed by 3 months of winter 8 hours dark, 16 hours light).  Juvenile sticklebacks were reared from fertilisation under 3 months of summer light cycle followed by 3 months of winter light cycle.  Testes and livers were collected during the last three weeks of the 3-month low light period, snap-frozen in liquid nitrogen, and stored in -80’C.

extract_protocol:
Tissue lysate was prepared from frozen tissue following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65.
The ChIP pulldown of DMC1-bound single stranded DNA was performed with "kinetic enrichment" following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65 and was followed sequentially by a ChIP pull down H3K4me3 on the same tissue lysate.

value: TestesPool

value: wild-derived freshwater strain


title: Lane1_Sample_47


title: SS-BMI1

description: ChIP


title: SS-CTCF

description: ChIP


title: Ctr-HDAC2

description: ChIP


title: DO-128_F_Islet


title: Group-II DCOR BUCCAL

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95228.gif

source_name: 825 ng of amplified monkey Group II DCOR BUCCAL cDNA

value: LCV

value: DCOR


title: DO-125_F_Islet


title: Ctr-HDAC1

description: ChIP


title: DO-126_F_Islet


title: DO-124_F_Islet


title: Ctr-SUZ12

description: ChIP


title: Lane1_Sample_44

value: Whole Blood

value: infected


title: DO-123_F_Islet


title: Lane1_Sample_43

value: Heart


title: DO-122_F_Islet


title: Ctr-SMC3

description: ChIP

value: BJ


title: Lane1_Sample_42

value: Balb/c


title: Control-fed, testis_3, 16 weeks administration

city: Gwangju

first: Gwidong

last: Han

address: GIST, Cheomdnagwagiro 123

department: School of Life Sciences

country: South Korea

institute: GIST

data_processing:
Data processed with Macrogen inc.
After alignment with HISAT2, transcrition quantification processed with read count, transcript length, and depth coverage.
Assembly: mm10
Supplementary files format and content: tab-delimited text file, include FPKM and TPM value for each sample

source_name: Testis

extract_protocol:
With TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, San Diego, CA, USA), libraries are prepared for sequencing.
Ribosomal RNA removement with a Ribo-Zero rRNA Removal Kit (Illumina) and random fragmentation are processed.

treatment_protocol: We designed chronic ethanol administration for 16 weeks. We daily administrate 10ml of the LDC liquid diet per head. Before experiment, we processed initial acclimatization for feeding liquid diet with the control LDC liquid diet for 5 days.

value: Testis

value: WT

value: Control-fed


title: SS-SMC3

description: ChIP

value: fibroblasts

value: wild type

value: SS18-SSX1 overexpression


title: Lane1_Sample_49


title: DO-121_F_Islet

value: pancreatic islet

value: 45% fat


title: Ctr-RAD21

description: ChIP

value: control


title: Lane1_Sample_40

value: naive


title: Ctr-H3K27me3

description: ChIP


title: Control-fed, testis_2, 16 weeks administration


title: Lane1_Sample_41


title: Ctr-CTCF

description: ChIP


title: DO-120_M_Islet


title: Control-fed, testis_1, 16 weeks administration


title: DO-119_M_Islet


title: Lane1_Sample_46


title: Lane1_Sample_39


title: Ethanol-fed, testis_3, 16 weeks administration

value: Ethanol-fed


title: Lane1_Sample_45


title: Ctr-BMI1

description: ChIP


title: Lane1_Sample_38


title: Ethanol-fed, testis_2, 16 weeks administration


title: Ctr-IMR90-H2AK119ub

description: ChIP

value: IMR-90 cell line


title: K202Q Mutation Replicate 3 RNA-seq

city: Shanghai

first: Chaowei

last: Sang

state: Shanghai Province

address: Songhu Road 2005

department: School of life science Fudan uniersity

institute: Fudan University

data_processing:
Sequenced reads were aligned to the hg38 Homo sapiens reference via software Hisat2 (v.2.0.1). Differential expression analysis was performed using the DESeq2 (v.1.26.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Cell line

growth_protocol: Cells were cultured in DMEM (Gibco) supplemented with 10% FBS (BI), 100 units ml−1 penicillin, and 100 μg ml−1 streptomycin (Sangon Biotech). Cells were maintained in an incubator at 37°C, 5% CO2.

extract_protocol:
1μg total RNA was extracted using TRIZOL (Life Technologies 15596018CN) from HeLa cells
Libraries were generated from the total RNA using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (VAHTS NR605).

value: Cell line

value: HeLa

value: HDAC8 K202Q Mutation


title: DO-116_M_Islet


title: K202Q Mutation Replicate 2 RNA-seq


title: Ethanol-fed, testis_1, 16 weeks administration


title: DO-115_M_Islet


title: Lane1_Sample_37

value: Whole Blood

value: infected

value: Heart


title: Lane1_Sample_36


title: K202Q Mutation Replicate 1 RNA-seq


title: Femoral end RNA from ethanol-fed mice of the Nox2 conditional knockout genotype. 3rd replicate

city: New Orleans

first: Kim

middle: B

last: Pedersen

state: LA

address: 1901 Perdido St., Rm 5206

department: Pharmacology and Exp. Therapeutics

institute: LSU Health Sciences Center, Dept. of Pharmacology

data_processing:
Information as provided by Azanta: "Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step."
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Femoral bone ends

extract_protocol:
Trireagent extraction followed by Rneasy Mini Spin column purification. Quality verified by Agilent tapestation analysis.
Permed by commercial vendor Azenta Life Sciences on Illumina HiSeq 4000 with Configuration HiSeq 2x150bp HiSeq 2x150bp

treatment_protocol: Female mice of two Nox2 genotypes (Conditional knockout and floxed control) were subjected to ethanol feeding or pair-feeding. Femurs were isolated and the shaft and marrow removed leaving the femoral end pieces, from which RNA was isolated.

value: Femoral bone ends

value: Conditional knockout


title: K202R Mutation Replicate 3 RNA-seq

value: HDAC8 K202R Mutation


title: DO-114_M_Islet


title: Femoral end RNA from ethanol-fed mice of the Nox2 conditional knockout genotype. 2nd replicate


title: DO-113_M_Islet


title: Lane1_Sample_35

value: Balb/c


title: DO-112_M_Islet


title: Femoral end RNA from ethanol-fed mice of the Nox2 conditional knockout genotype. 1st replicate


title: Lane1_Sample_32


title: K202R Mutation Replicate 1 RNA-seq


title: DO-118_M_Islet


title: Femoral end RNA from pair-fed mice of the Nox2 conditional knockout genotype. 3rd replicate

value: Pair-fed


title: DO-111_M_Islet

value: pancreatic islet


title: K202R Mutation Replicate 2 RNA-seq


title: Wild Type Replicate 3 RNA-seq

value: Wild Type


title: Lane1_Sample_33


title: Femoral end RNA from pair-fed mice of the Nox2 conditional knockout genotype. 1st replicate


title: Wild Type Replicate 2 RNA-seq


title: DO-108_M_Islet

value: 45% fat


title: Lane1_Sample_29


title: Femoral end RNA from ethanol-fed mice of the control floxed genotype. 3rd replicate

value: Floxed control


title: Lane1_Sample_28

value: naive


title: DO-107_M_Islet


title: Wild Type Replicate 1 RNA-seq


title: DO-106_M_Islet


title: Femoral end RNA from ethanol-fed mice of the control floxed genotype. 2nd replicate

value: Ethanol-fed


title: Femoral end RNA from ethanol-fed mice of the control floxed genotype. 1st replicate


title: DO-105_M_Islet


title: K202Q Mutation Replicate 2 HiC

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v3.1 (Servant et al., 2015). Reads were processed by Juicebox-pre (juicer tools v.1.9.9, Durand et al. 2016) to generate Juicebox-ready files.
Assembly: hg19
Supplementary files format and content: .hic file (contains contact matrices at various resolutions)

extract_protocol:
Hi-C libraries were prepared using in situ Hi-C protocol as previously described (Rao et al., 2014) with some modifications. In brief, 0.2 to 0.5 million HeLa cells were crosslinked with 16% formaldehyde (Thermo 28908) to a final concentration of 1% for 10 min at room temperature, followed by quenched by 0.2 M glycine for 5 min. Cell nuclei were extracted with lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% Igepal CA630) mixed with 50× protease inhibitor (Sigma P8340) on ice for at least 15 min. Cell pellets were resuspended in 0.5% SDS (prepared from 10% SDS  (Sigma 71736)) and incubated at 62°C for exactly 10 min, then quenched with 1.5% trix-100 (freshly prepared from 10% Triton X-100 (Sigma 648463)) for 15 min at 37°C. DNA was then digested with Dpn II restriction enzyme (NEB R0543L) for 16h at 37°C, followed by an incubation at 62°C for 20 minutes. End repair of DNA as well as biotin labeling was achieved by incubation at 37° for 1h in the fill-in master mix (with a final concentration of 0.4mM biotin-14-dATP (Invitrogen 19524016), 3.3 mM dCTP, 3.3 mM dGTP, 3.3 mM dTTP, 5000U/mL DNA Polymerase I, Large (Klenow) Fragment (NEB M0210L)). DNA was then ligated by incubation in a ligation master mix (composed of 664ul of water, 120μl of 10X T4 DNA ligase buffer (NEB B0202), 100μl of 10% Triton X-100 (Sigma 71736), 6μl of 20mg/ml Bovine Serum Albumin (Sigma B8667), and 10μl of 400 U/ μl T4 DNA Ligase (NEB M0202)) at room temperature with low-speed rotation for 4h. Cell pellets were resuspended in 300 μL of PK digestion buffer (10 mM Tris-HCl pH8.0, 0.5 M NaCl, 1% SDS), followed by the addition of 50 μL of 20mg/ml proteinase K (QIAGEN 19133). The mixture was digested at 55°C for 30 minutes to uncross-link the DNA, and then incubated overnight at 68°C. To efficiently purify the DNA, the TIANamp Genomic DNA Kit (TIANGEN DP304) was used instead of low-temperature precipitation with ethanol and sodium acetate. Sonication was then employed to break DNA into an average size of 300-500 bp. Biotin-labeled DNA was pulled down with Dynabeads MyOne Streptavidin C1 beads (Invitrogen 65001) and prepped for library construction.
Libraries were constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme ND607) following the instructions.

value: Cell line


title: Lane1_Sample_27


title: Lane1_Sample_31


title: Femoral end RNA from pair-fed mice of the control floxed genotype. 3rd replicate


title: DO-104_M_Islet


title: Femoral end RNA from pair-fed mice of the control floxed genotype. 2nd replicate


title: K202R Mutation Replicate 1 HiC

value: HeLa


title: Femoral end RNA from pair-fed mice of the Nox2 conditional knockout genotype. 2nd replicate


title: Lane1_Sample_24


title: Lane1_Sample_26


title: K202R Mutation Replicate 2 HiC


title: Femoral end RNA from pair-fed mice of the control floxed genotype. 1st replicate


title: DO-109_M_Islet


title: Lane1_Sample_25


title: DO-103_M_Islet


title: Lane1_Sample_23


title: Lane1_Sample_30


title: DO-101_M_Islet


title: CD44hi AT2 cells

city: Chicago

first: Qian

last: Chen

state: IL

address: 909 S Wolcott avenue, COMRB 4160

department: Department of Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.0/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
AT2 cells were isolated from 6 SpcER/Tomato/zsGreen mice and pooled together. Using FACS, cells were sorted into total AT2 (zsGreen+) and CD44hi AT2 (zsGreen+CD44hi) populations and resuspended in DMEM + 30% FBS.  Cells were washed twice with 1.5 ml ice cold PBS + 10% FBS and finally resuspended in PBS. Cell number and viability was determined by an automated cell counter as well as by manual counting using Trypan Blue dye.
The single cell library preparation and sequencing was done at Northwestern University NUseq core facility with the support of NIH Grant (1S10OD025120).  Cell number and viability were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. Sixteen thousand cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip G (10X Genomics, PN-1000120), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on Illumina HiSeq 4000 sequencer with 2 × 50 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript.

value: AT2 cells

value: Lung

value: SpcER/Tomato/zsGreen

tag: age

value: 6-8 weeks old


title: Lane1_Sample_22

value: Whole Blood

value: infected

value: Heart


title: SCA34_T2

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

data_processing:
Read quality was assessed using FastQC v0.11.9
Raw reads were trimmed and filtered by quality score of 15 and Truseq adapter sequences were removed using Trimmomatic v0.39
Trimmed reads were mapped using Hisat2 v2.2.1 and reference index grch38
Aligned Bam files were processed to Samtools v1.10
Gene Expression was quantified using Subread v2.0.1 FeatureCounts v1.5.0-p3 for raw counts
Assembly: grch38
Supplementary files format and content: all_merged.txt.gz: tab delimited file, raw counts of all samples

molecule: polyA RNA

source_name: Whole blood

extract_protocol: RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

tag: health status

value: sickle cell anemia (SCA)

value: Whole blood

value: time 2

tag: exercise intensity

value: moderate

tag: Sex

value: female


title: Wild Type Replicate 1 HiC

tag: tissue

tag: genotype

value: Wild Type


title: K202Q Mutation Replicate 1 HiC

value: HDAC8 K202Q Mutation


title: Wild Type Replicate 2 HiC


title: DO-100_M_Islet

value: pancreatic islet

value: 45% fat


title: Lane1_Sample_20

value: naive

value: Balb/c


title: DO-099_M_Islet


title: SCA34_T1

tag: time

value: time 1


title: spatial transcriptomics of normal tissue of patient 1

first: guangyong

last: zheng

address: cailun road 1200

institute: shutcm

description: fresh frozen spatial transcriptome sequencing

data_processing:
raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate fastq files
sequences were aligned to GRCh 38 genome for gene experssion counting using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh 38
Supplementary files format and content: p1_N.barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: p1_N.features.tsv.gz list of gene IDs
Supplementary files format and content: p1_N.matrix.mtx.gz gene expression count data in matrix market exchange format
Supplementary files format and content: p1_N.aligned_fiducials.jpg aligned fiducials of the tissue image
Supplementary files format and content: p1_N.detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: p1_N.scalefactors_json.json scalefactors in json format
Supplementary files format and content: p1.tissue_hires_images.png hi-res image of tissue
Supplementary files format and content: p1.tissue_lowres_image.png low-res image of tissue
Supplementary files format and content: p1_N.tissue_position_list.csv list of spatial barcodes and the coordinates sepecifying spots
Library strategy: Spatial Transcriptomics

source_name: colon

extract_protocol:
fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expresssion Slides & Reagent kit according to manufacture's instruction

value: colon

tag: patient diagnosis

value: mucinous colorectal adenocarinoma

tag: disease state

value: normal


title: shLacZ20-input

city: Charleston

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence (Cutadapt), and masked for low-complexity or low-quality sequence (FASTQC)
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated ChIPseq workflow to process the data, including data validation, quality control and read alignment to the HUMAN genome (hg19) using bowtie2
The resulting SAM files were sorted and inputted into the MACS2 peak calling program in the broad mode  to generate peaks data including significance scoring.
MACS2 Peaks were mapped to genes using the HOMER Tools AnnotatePeaks.pl script.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt files include MACS2 output for each Sample.

source_name: SUM-44PE breast cancer cells

growth_protocol: Cells were cultured at 37°C in 10% CO2 and passaged using Trypsin (Invitrogen Catalog # 15400-054) diluted to 1x with Hanks Buffered Salt Solution (Corning Cellgro Catalog #20-021-CV) supplemented with 1 ml/L sodium bicarbonate and 25 μg/ml gentamicin. SUM-44 cells were cultured in serum-free Ham’s F-12 medium supplemented with 1 μg/ml hydrocortisone, 1 mg/ml bovine serum albumin, 10 mM HEPES, 5 mM ethanolamine, 5 μg/ml transferrin, 10 nM triiodothyronine, 50 nM sodium selenite, 25 μg/ml gentamicin, 2.5 μg/ml fungizone, and 5 μg/ml insulin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared from ChIP DNA by the MUSC Genomics Core Facility with Rubicon ThruPLEX library preparation kits and sequenced as 35 bp single-end reads on an Illumina HiSeq 2500. Libraries for three biological replicates were prepared and sequenced for each sample type.

treatment_protocol: Target cells were transduced with virus in growth media supplemented with 5 μg/ml polybrene using 0.5-1.0 ml virus per 1 million cells. Cells were selected for resistance marker expression and maintained in puromycin-containing growth media beginning 24-48 hours after infection. Cells were cultured in selection media at least 5 days to allow expression of the construct. 3 μg/ml puromycin was used for selection and maintenance of shRNA-transduced SUM-44 cells.

tag: passage

tag: source

value: pleural effusion cells from metastatic ER+ breast cancer patient

tag: antibody

tag: transduction


title: SCA32_T2

value: vigorous

value: male


title: Lane1_Sample_19

source_name: Whole Blood

value: Whole Blood

tag: mouse

tag: cage

tag: strain

value: Heart


title: DO-102_M_Islet

tag: diet


title: DO-098_M_Islet


title: SCA32_T1

value: sickle cell anemia (SCA)

value: Whole blood

tag: age


title: shLacZ19-input


title: Lane1_Sample_18

value: infected


title: DO-096_M_Islet


title: DO-097_M_Islet


title: shLacZ20-H3K4me3


title: shLacZ19-H3K4me3


title: SCA31_T2

tag: health status

value: time 2

value: female


title: Total AT2 cells

description: 10x Genomics

tag: cell type

value: AT2 cells

value: Lung

value: SpcER/Tomato/zsGreen

value: 6-8 weeks old


title: DO-095_M_Islet

value: pancreatic islet

value: 45% fat


title: SCA31_T1

value: time 1

tag: exercise intensity

tag: Sex


title: shLacZ18-input

value: pleural effusion cells from metastatic ER+ breast cancer patient


title: SCA29_T2

tag: tissue

value: vigorous


title: Lane1_Sample_16


title: Lane1_Sample_21

value: naive

value: Balb/c


title: shLacZ18-H3K4me3


title: SCA29_T1

tag: time


title: Lane1_Sample_14

value: Whole Blood

value: Heart


title: shASH2L-input


title: DO-091_M_Islet


title: DO-090_M_Islet


title: SCA28_T1

value: sickle cell anemia (SCA)

value: Whole blood

value: moderate

value: male


title: shASH2L-H3K4me3


title: Lane1_Sample_13


title: SCA27_T2

value: time 2


title: DO-089_M_Islet


title: Lane1_Sample_12


title: Lane1_Sample_17

value: infected


title: SCA27_T1


title: shASH2L-B-input


title: Lane1_Sample_10


title: Lane1_Sample_11


title: shASH2L-A-input


title: shASH2L-B-H3K4me3


title: SCA26_T2

value: female


title: DO-094_M_Islet


title: Lane1_Sample_15


title: DO-087_M_Islet


title: DO-088_M_Islet


title: Lane1_Sample_9


title: SCA26_T1


title: DO-092_M_Islet


title: DO-086_M_Islet


title: Lane1_Sample_6


title: ChIPseq_H3K4me3_Input_sticklebackTestesPool_Freshwater

value: TestesPool

value: wild-derived freshwater strain


title: SCA28_T2


title: SCA23_T2


title: DO-085_M_Islet

value: pancreatic islet

value: 45% fat


title: ChIPseq_H3K4me3_sticklebackTestesPool_Freshwater


title: SCA23_T1

value: time 1


title: DO-084_M_Islet


title: Lane1_Sample_4


title: Radiation, replicate 3, 100 days, bulk RNAseq

city: Beijing

first: Ziming

last: Jiang

address: 17 Panjiayuan Nanli Chaoyang District

department: Department of Thoracic Surgery

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

data_processing:
Fastp software (https://github.com/OpenGene/fastp) is used to joint sequences, filter low-quality and N-base, and obtain high-quality clean data. For the analysis of differentially expressed genes, the clean data for each sample were aligned to the mus musculus reference genome (https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.27_GRCm39/GCF_000001635.27_GRCm39_genomic.fna.gz) using STAR (version 2.7.6a) software. We used StringTie2 software to quantify gene expression levels and standardized the expression levels using FPKM (Fragments per Kilobase Million) and TPM (Transcripts Per Million) methods. We calculated the differential expression levels and evaluated the statistical significance of detected genes by using DESeq2 software. Genes were considered as significantly differentially expressed with false discovery rates (FDRs) ≤0.05 and |log2 fold-changes| >1.0.
Supplementary files format and content: Tab-delimited text files, including FPKM and TPM normalized counts for each sample

extract_protocol: Total RNA was extracted from each sample of lung tissue (control group or irradiation group) using TRIzol reagent according to the manufacturer’s protocol (Invitrogen, California). The RNA was quantified using a NanoDrop spectrophotometer (Thermo, California). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number > 7.0, and confirmed by electrophoresis with denaturing agarose gel. For RNA high-throughput sequencing, mRNA libraries were created from each group using the Hieff NGS MaxUp ll Dual-mode mRNA library prep kit from Illumina (San Diego, CA), and sequenced by DNBSEQ-T7 (GenePlus-Shenzhen, Shenzhen, China).

value: Lung

tag: cell line

value: Whole tissue

tag: genotype

value: WT

tag: treatment

value: 20 Gy

tag: timepoint

value: 100 days


title: Lane1_Sample_3

value: Whole Blood

value: naive

value: Balb/c

value: Heart


title: DO-083_M_Islet


title: SCA22_T2

value: sickle cell anemia (SCA)

value: Whole blood

value: time 2

value: moderate


title: SCA22_T1

value: female


title: DO-082_M_Islet

value: pancreatic islet


title: shASH2L-A-H3K4me3

tag: passage

tag: source

value: pleural effusion cells from metastatic ER+ breast cancer patient

tag: antibody


title: DO-081_M_Islet

value: 45% fat


title: Lane1_Sample_1

tag: mouse

tag: cage

value: infected


title: Radiation, replicate 1, 100 days, bulk RNAseq

tag: strain

value: Lung

value: Whole tissue


title: Lane1_Sample_2


title: Control, replicate 3, 100 days, bulk RNAseq

value: WT

value: Control


title: DO-080_M_Islet

tag: diet


title: SCA18_T2

tag: health status

tag: age


title: Control, replicate 2, 100 days, bulk RNAseq

value: 100 days


title: SCA19_T1

value: time 1

tag: exercise intensity

value: vigorous


title: post-MBT RNA-seq rep2

city: Salt Lake City

first: Bradley

middle: R

last: Cairns

state: UT

address: 2000 Cir of Hope Dr

department: oncological Sciences

institute: Huntsman Cancer institute/HHMI

data_processing:
Raw reads were aligned to zv10 using Novoalign ( v2.8 novocraft) with the options [-o Sam -r All 50 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT]
Bam files were generated using the SamTranscriptomeParser from the Useq packages (v8.8.8 default parameters)
FPKM were calculated using the DefinedRegionDifferentialSeq from the Useq packages (v8.8.8 default parameters), which uses the DESeq2 R package for variance normalization and differential expression analysis.
Genome_build: zv10
Supplementary_files_format_and_content: text files contains the FPKM values of the each replicate at MBT or post-MBT stages.

organism: Danio rerio

source_name: post-MBT zebrafish embryo

growth_protocol: Zebrafish (strain Tübingen)  embryos were incubated at 28C

extract_protocol:
RNA was extracted from dechorinated and deyolked zebrafish embryos (4 hpf (MBT) and 5.3 hpf (post-MBT) ) using the Norgen Animal and Tissue RNA Extraction Kit (#25700) according to the manufacturer's instructions including the optional step of DNAse I treatment.
5ng of purified, total RNA was used to produce RNAseq libraries for each sample using the EpiCentre TotalScript™ RNA-Seq Kit (#TSRNA12924). Briefly, total RNA was reverse-transcribed using random hexamer primers, followed by second-strand synthesis and adapter addition via tagmentation. The final RNA-Seq library was amplified by PCR for a total of 10 cycles.

value: Tubingen

value: embryo

tag: developmental stage

value: 30% epiboly stage


title: Control, replicate 1, 100 days, bulk RNAseq

tag: Sex

tag: tissue


title: post-MBT RNA-seq rep1


title: SCA18_T1

value: sickle cell anemia (SCA)

value: Whole blood

tag: time


title: DO-078_M_Islet

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.


title: DO-079_M_Islet


title: Lane1_Sample_5

value: Whole Blood

value: Heart


title: Radiation, replicate 2, 100 days, bulk RNAseq

value: female

tag: cell line

tag: genotype

value: 20 Gy


title: SCA17_T2

value: time 2

value: male


title: MBT RNA-seq rep1

source_name: MBT zebrafish embryo

value: sphere stage


title: DO-075_M_Islet

source_name: pancreatic islet

value: pancreatic islet

value: 45% fat


title: MBT RNA-seq rep2


title: SCA17_T1


title: SCA19_T2


title: DO-076_M_Islet


title: Whole blood Animal PA75 at D119 after full length CyCMV/flu vaccination

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Sequenced reads were trimmed with Trim galore using default parameters version 0.6.4
Globin and rRNA reads filtered out with bowtie2 version 2.4.2
Reads aligned and quantified using STAR v 2.7.5 to rhesus macaque genome version10 with ensembl annotation version 100
Assembly: rhesus macaque genome version10 with ensembl annotation version 100
Supplementary files format and content: count_matrix.txt

organism: Macaca fascicularis

source_name: Whole Blood PAXgene

extract_protocol:
Whole blood was collected from cynomolgus macaques in PAXgene RNA tubes (PreAnaytiX) to manufacturers instrucruction. RNA was isolated using RNAdvance Blood Kit with the manufacter's instructions
Libraries were constructed using Illumina TruSeq Stranded mRNA HT kit

treatment_protocol: Cynomolgus macaques received subcutanous adminstration of a prime and boost of either the  68-1 CyCMV/flu or  full length 68-1 CyCMV/flu vaccines

tag: time point

tag: vaccination outcome

value: Non protected

value: Male

tag: animall id

value: Whole Blood PAXgene

tag: treatment

value: full length CyCMV/flu


title: Whole blood Animal PA73 at D119 after full length CyCMV/flu vaccination

value: Deceased

value: Female


title: Whole blood Animal PA69 at D119 after full length CyCMV/flu vaccination

value: Protected


title: SCA16_T1

value: sickle cell anemia (SCA)

value: Whole blood

value: time 1

value: vigorous


title: DO-072_M_Islet


title: Whole blood Animal PA67 at D119 after full length CyCMV/flu vaccination


title: DO-073_M_Islet


title: Whole blood Animal PA65 at D119 after full length CyCMV/flu vaccination


title: SCA16_T2


title: SCA15_T2

value: female


title: MBT PolII Flav ChIP-seq

description:
MBT_PolII_flav_peaks.txt
MBT_PolII_flav.bw

data_processing:
Raw reads were aligned to zv10 using Novoalign ( v2.8 novocraft) with the options [-r None -k -Q 13 -o SAM]
Sam files were converted to bam files using samtools.
Sorted bam files of replicates were then merged using MergeSamFiles.jar from Picard tools (v 1.100)
Peaking calling, relative to paired input, was performed using MACS2 (v2.1.0.20140616), using the following parameters: -f BAM -g 1.4e9 -B --fix-bimodal --extsize 250 -q 0.01
treat_pileup.bdg files from macs2 were then converted to bigWig files using bedGraphtoBigWig
Genome_build: zv10
Supplementary_files_format_and_content: text files are peak profiles generated from MACS2, and bigWig files represent the genome-wide protein occupancy

source_name: Flavopiridol treated MBT zebrafish embryo

growth_protocol: Zebrafish embryos (strain Tübingen) were incubated at 28C

extract_protocol:
Nuclei from formaldehyde crosslinked (1%; 10min at room temperature) embryos were isolated and chromatin was fragmented using sonicator (Branson). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and Dynabeads. DNA fragments were purified and libraries were prepared by NEBnext DNA Library Prep Kit (NEB, E7370L). Adapter ligated DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and sequenced by illumina HiSeq 2500.
NEBnext DNA Library Prep Kit

treatment_protocol: 4 datasets were generated from flavopiridol treated emrbyos. Embryos were dechorinated immediately after fertilization, and closely monitored for the development stages. Flavopiridol (Sigma-Aldrich F3055) were added to the embryo water to a final concentration of 10uM to inhibit transcription elongation at 3.75hpf, and the embryos then were collected at sphere stage.

value: Tubingen

value: embryo

tag: developmental stages

tag: chip antibody

value: Covance MMS-126R


title: MBT RNA-seq rep3

tag: strain

value: sphere stage


title: Whole blood Animal PA64 at D119 after full length CyCMV/flu vaccination


title: MBT Brm Flav ChIP-seq

description:
MBT_Brm_flav_peaks.txt
MBT_Brm_flav.bw

value: Customized Brm polyclonal antibody


title: DO-070_F_Islet

value: pancreatic islet

tag: diet

value: 45% fat


title: Whole blood Animal PA77 at D119 after 68-1 CyCMV/flu vaccination

value: Male

value: Whole Blood PAXgene

value: 68-1 CyCMV/flu


title: DO-069_F_Islet


title: SCA14_T2

tag: health status

value: time 2

value: moderate

value: male


title: DO-071_M_Islet


title: SCA15_T1

value: sickle cell anemia (SCA)

value: Whole blood

tag: age


title: Whole blood Animal PA72 at D119 after 68-1 CyCMV/flu vaccination

value: Protected

value: Female


title: post-MBT input DNA

value: Tubingen

value: 30% epiboly stage


title: Whole blood Animal PA71 at D119 after 68-1 CyCMV/flu vaccination


title: DO-068_F_Islet


title: SCA13_T2

tag: exercise intensity


title: MBT H3K36me3 Flav ChIP-seq

description:
MBT_H3K36me3_flav_peaks.txt
MBT_H3K36me3_flav.bw

value: embryo

value: Abcam 4074


title: SCA14_T1

value: time 1


title: Whole blood Animal PA70 at D119 after 68-1 CyCMV/flu vaccination

value: Non protected


title: post-MBT PolII ChIP-seq rep2

description:
postMBT_PolII_peaks.txt
postMBT_PolII.bw

value: Covance MMS-126R


title: SCA13_T1


title: post-MBT PolII ChIP-seq rep1


title: DO-066_F_Islet

value: pancreatic islet

value: 45% fat


title: post-MBT Brm ChIP-seq rep2

description:
postMBT_Brm_peaks.txt
postMBT_Brm.bw

value: Customized Brm polyclonal antibody


title: Whole blood Animal PA63 at D119 after 68-1 CyCMV/flu vaccination

value: Male

value: Whole Blood PAXgene

value: 68-1 CyCMV/flu


title: SCA12_T2

value: sickle cell anemia (SCA)

value: time 2

value: vigorous

value: male


title: Whole blood Animal PA62 at D119 after 68-1 CyCMV/flu vaccination

value: Protected


title: SCA12_T1

value: Whole blood


title: DO-065_F_Islet


title: post-MBT Brm ChIP-seq rep1

description:
postMBT_Brm_peaks.txt
postMBT_Brm.bw

value: Tubingen

value: embryo

value: 30% epiboly stage


title: DO-064_F_Islet


title: SCA09_T2

value: female


title: post-MBT Brg1 ChIP-seq rep3

description:
postMBT_Brg1_peaks.txt
postMBT_Brg1.bw

value: Customized Brg1 polyclonal antibody


title: post-MBT Brg1 ChIP-seq rep2

description:
postMBT_Brg1_peaks.txt
postMBT_Brg1.bw


title: Whole blood Animal PA73 at D108 after full length CyCMV/flu vaccination

value: Deceased

value: Female

value: full length CyCMV/flu


title: Whole blood Animal PA75 at D108 after full length CyCMV/flu vaccination

value: Non protected

value: Male


title: MBT Flav input DNA

value: sphere stage


title: SCA08_T2

value: sickle cell anemia (SCA)


title: DO-067_F_Islet

value: pancreatic islet

value: 45% fat


title: DO-061_F_Islet


title: DO-060_F_Islet


title: post-MBT Brg1 ChIP-seq rep1

description:
postMBT_Brg1_peaks.txt
postMBT_Brg1.bw


title: SCA05_T2

value: time 2

value: moderate


title: Whole blood Animal PA67 at D108 after full length CyCMV/flu vaccination

value: Whole Blood PAXgene


title: SCA08_T1

value: Whole blood

value: time 1

value: vigorous

value: male


title: Whole blood Animal PA69 at D108 after full length CyCMV/flu vaccination

value: Protected


title: DO-062_F_Islet


title: MBT PolII ChIP-seq rep1

description:
MBT_PolII_peaks.txt
MBT_PolII.bw

value: Tubingen

value: embryo

value: Covance MMS-126R


title: MBT input DNA


title: MBT PolII ChIP-seq rep2

description:
MBT_PolII_peaks.txt
MBT_PolII.bw


title: DO-059_F_Islet


title: SCA05_T1

value: female


title: Whole blood Animal PA65 at D108 after full length CyCMV/flu vaccination

value: Male

value: full length CyCMV/flu


title: MBT Brm ChIP-seq rep2

description:
MBT_Brm_peaks.txt
MBT_Brm.bw

value: sphere stage

value: Customized Brm polyclonal antibody


title: DO-058_F_Islet

value: pancreatic islet

value: 45% fat


title: Whole blood Animal PA77 at D108 after 68-1 CyCMV/flu vaccination

value: 68-1 CyCMV/flu


title: SCA04_T2

value: sickle cell anemia (SCA)

value: time 2


title: Whole blood Animal PA64 at D108 after full length CyCMV/flu vaccination

value: Non protected

value: Whole Blood PAXgene


title: DO-056_F_Islet


title: MBT Brg1 ChIP-seq rep2

description:
MBT_Brg1_peaks.txt
MBT_Brg1.bw

value: Customized Brg1 polyclonal antibody


title: DO-063_F_Islet


title: Whole blood Animal PA72 at D108 after 68-1 CyCMV/flu vaccination

value: Protected

value: Female


title: DO-057_F_Islet


title: Whole blood Animal PA71 at D108 after 68-1 CyCMV/flu vaccination


title: MBT Brm ChIP-seq rep1

description:
MBT_Brm_peaks.txt
MBT_Brm.bw

value: Tubingen

value: embryo


title: SCA04_T1

value: Whole blood

value: time 1

value: vigorous

value: male


title: SCA09_T1

value: female


title: SCA03_T2

value: moderate


title: DO-055_F_Islet

value: pancreatic islet

value: 45% fat


title: DO-054_F_Islet


title: Whole blood Animal PA63 at D108 after 68-1 CyCMV/flu vaccination

value: Male

value: 68-1 CyCMV/flu


title: SCA01_T1

value: sickle cell anemia (SCA)


title: pre-MBT input DNA

source_name: pre-MBT zebrafish embryo

value: 256-cell stage


title: pre-MBT PolII ChIP-seq

description:
preMBT_PolII_peaks.txt
preMBT_PolII.bw

value: Covance MMS-126R


title: Whole blood Animal PA62 at D108 after 68-1 CyCMV/flu vaccination

value: Protected

value: Whole Blood PAXgene


title: SCA01_T2

value: time 2


title: Whole blood Animal PA70 at D108 after 68-1 CyCMV/flu vaccination

value: Non protected


title: SCA03_T1

value: Whole blood


title: pre-MBT Brm ChIP-seq

description:
preMBT_Brm_peaks.txt
preMBT_Brm.bw

value: Tubingen

value: embryo

value: Customized Brm polyclonal antibody


title: Whole blood Animal PA75 at D105 after full length CyCMV/flu vaccination

value: full length CyCMV/flu


title: DO-052_F_Islet


title: pre-MBT Brg1 ChIP-seq

description:
preMBT_Brg1_peaks.txt
preMBT_Brg1.bw

value: Customized Brg1 polyclonal antibody


title: DO-051_F_Islet

value: pancreatic islet


title: CON22_T1

value: healthy control (CON)

value: time 1

value: moderate

value: male


title: CON22_T2


title: Whole blood Animal PA73 at D105 after full length CyCMV/flu vaccination

value: Deceased

value: Female


title: Wing disc, CrGFP-HP1chromo, GFP, rep3, sup

city: Chapel Hill

first: Alexis

last: Stutzman

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Fastq files for biological replicates were combined. Adapters were trimmed using bbmap version 38.71 and parameters ktrim=k, ref=adapters, rcomp=t, tpe=t, tbo=t, hdist=1, mink=11 for all fastq files (individual replicates and merged fastq files). Trimmed reads were aligned to the dm6 reference genome using bowtie2 version 2.3.4.1 and parameters --seed 123 -q --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 400. Sam files were then converted to bam files and reads were filtered using samtools version 1.10 such that only reads with a MAPQ greater than 5 were kept. Bam files were sorted using samtools and converted to bed files using bedtools version 2.26. Read depth was calculated and rpgc-normalized bedgraphs were generated from bed files using bedtools. Bedgraphs were converted to bigWigs using ucsctools version 320. Peaks were called from bed files using macs2 version 2.1.2 with parameters --nomodel, --seed 123. As a control for peak calling, we used sonicated genomic DNA.
Peak calls from negative control experiments were used to create a list of blacklisted peaks for each experimental antibody, which were filtered out of experimental data using the bedtools function intersect with option -v at the bam to bed file conversion step. Peaks called from IgG CUT&RUN were used in blacklists for all experiments. Peak calls from additional negative control experiments were combined with IgG peak calls to create specific blacklists for each experiment, as follows. For C1A9 HP1a CUT&RUN, only IgG peaks were blacklisted. For GFP-HP1a CUT&RUN, peaks called from anti-GFP CUT&RUN on yw wing imaginal discs, which lack the GFP epitope, were combined with IgG peaks. For H3K9me3 CUT&RUN, we examined the possibility that loss of the H3K9me3 epitope in H3.2K9R wings resulted in cross-reactivity of the H3K9me3 antibody with H3K27me3 due to similarity in the surrounding amino acids80. Comparison of H3K9me3 and H3K27me3 signals in H3.2HWT and H3.2K9R CUT&RUN showed evidence of cross-reactivity (Figure S3F-G). Therefore, we included peaks called from H3K27me3 CUT&RUN in the blacklist for H3K9me3 CUT&RUN. H3.2HWT H3K27me3 was used to blacklist H3.2HWT H3K9me3, H3.2K9R H3K27me3 was used to blacklist H3.2K9R H3K9me3, and yw H3K27me3 was used to blacklist HP1acontrol and HP1achromo H3K9me3 profiles.
Assembly: dm6
Supplementary files format and content: CrGFP-HP1a_3LW-wing_GFP-CnR.bw
Supplementary files format and content: CrGFP-HP1chromo_3LW-wing_GFP-CnR.bw

organism: Drosophila melanogaster

source_name: wing disc

growth_protocol: Stocks were maintained on standard cornmeal food at 25˚C. H3.2HWT and H3.2K9R larvae were cultured as previously described in Penke 2016. Briefly, one hundred fifty yw; ∆HisC, twi-Gal4/CyO virgin females and seventy-five yw; ∆HisC, UAS-2xEYFP/CyO; H3.2HWT/ H3.2HWT or H3.2K9R/ H3.2K9R males were put in a cage and allowed to lay eggs on a grape juice agar plates. GFP-positive L1 larvae were transferred to vials of standard food and allowed to grow at 25˚C. Wandering third instar (L3) GFP-positive larvae were used for experiments. HP1acontrol and HP1achromo larvae were cultured by establishing vials with ten w1118; Df(2L)BSC228/CyO, Tb, RFP virgin females and, to produce HP1acontrol, a single yw; +; + male, or a single w1118; HP1achromo/CyO, Tb, RFP male (Table S3). After three days, genomic DNA from sacrificed w1118; HP1achromo/CyO, Tb, RFP males was sequenced to confirm the genotype the HP1achromo allele, which exhibits occasional instability. The remaining females were flipped daily and non-tubby third larval instar wandering females were used for experiments.

extract_protocol:
A minimum of 20 wing imaginal discs per replicate were dissected from wandering female L3 larvae and used as input for CUT&RUN, as described previously (Ahmad 2018). The following antibody concentrations were used in CUT&RUN experiments: 1:100 anti-H3K9me3 (Abcam ab8898), 1:100 anti-HP1a (Developmental Studies Hybridoma Bank C1A9), 1:100 anti-GFP (Rockland 600-401-215), 1:100 anti-H3K27me3 (Cell Signal Technology #9733s), and 1:100 protein A/G-MNase. Using expression vector from Addgene (plasmid #123461), protein A/G-MNase was produced by the UNC Protein Expression and Purification Core using a published protocol (Meers 2019).
Libraries were prepared using Takara ThruPLEX DNA-Seq Kit (R400675) with Takara DNA Unique Dual Index Kit (R400665R, R400666R, R400667R, R400668R).

value: wing disc

tag: cut&run antibody

value: yw; CrGFP-HP1chromo/Cyo, Tb, RFP; +


title: DO-050_F_Islet

value: 45% fat


title: Whole blood Animal PA69 at D105 after full length CyCMV/flu vaccination

value: Protected

tag: Sex

value: Male

value: Whole Blood PAXgene


title: Wing disc, CrGFP-HP1chromo, GFP, rep2, sup

tag: tissue


title: DO-049_F_Islet


title: Whole blood Animal PA67 at D105 after full length CyCMV/flu vaccination

value: Non protected


title: CON21_T1

value: Whole blood

tag: time

value: vigorous


title: DO-048_F_Islet


title: MBT Brg1 ChIP-seq rep1

description:
MBT_Brg1_peaks.txt
MBT_Brg1.bw

value: Tubingen

value: embryo

value: sphere stage

value: Customized Brg1 polyclonal antibody


title: DO-053_F_Islet

value: pancreatic islet


title: Whole blood Animal PA65 at D105 after full length CyCMV/flu vaccination

value: full length CyCMV/flu


title: DO-047_F_Islet


title: CON20_T2

value: healthy control (CON)

value: time 2

value: male


title: Whole blood Animal PA64 at D105 after full length CyCMV/flu vaccination


title: DO-046_F_Islet


title: CON20_T1

value: time 1


title: Wing disc, CrGFP-HP1a, GFP, rep3, sup

value: wing disc

value: yw; CrGFP-HP1a; +


title: CON19_T2

value: moderate

value: female


title: Wing disc, CrGFP-HP1a, GFP, rep2, sup


title: CON21_T2


title: Wing disc, CrGFP-HP1a, GFP, rep1, sup


title: Whole blood Animal PA72 at D105 after 68-1 CyCMV/flu vaccination

value: Protected

value: Female

value: Whole Blood PAXgene

value: 68-1 CyCMV/flu


title: CON19_T1

value: Whole blood


title: DO-042_F_Islet

value: 45% fat


title: Whole blood Animal PA71 at D105 after 68-1 CyCMV/flu vaccination

value: Male


title: Wing disc, HP1a-chromo, FAIREseq, rep3

data_processing:
Files were merged at the fastq level. Adapters were trimmed using bbmap version 38.71 and parameters ktrim=k ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11. Trimmed reads were aligned to dm6 using bowtie2 version 2.3.4.1 and default parameters with --seed 123. Sam files were then converted to bam files and reads were filtered using samtools version 1.9 such that only reads with a MAPQ greater than 5 were kept. Duplicates were marked using picard version 2.2.4 and removed using samtools. Bam files for biological reps were pooled using samtools. All bam files were converted to bed files using bedtools version 3.36. Read depth was calculated and rpgc-normalized bigWigs were generated from bed files using deeptools version 2.4.1.
Assembly: dm6

growth_protocol: Stocks were maintained on standard cornmeal food at 25˚C. HP1acontrol and HP1achromo larvae were cultured by establishing vials with ten w1118; Df(2L)BSC228/CyO, Tb, RFP virgin females and, to produce HP1acontrol, a single yw; +; + male, or a single w1118; HP1achromo/CyO, Tb, RFP male (Table S3). After three days, genomic DNA from sacrificed w1118; HP1achromo/CyO, Tb, RFP males was sequenced to confirm the genotype the HP1achromo allele, which exhibits occasional instability. The remaining females were flipped daily and non-tubby third larval instar wandering females were used for experiments.

extract_protocol:
A minimum of 50 wing imaginal discs per replicate were dissected from wandering female L3 w1118; HP1achromo/Df or w1118; Df/+ (HP1acontrol) larvae and used as input for FAIRE-seq, as described previously (Uyehara 2022).
Libraries were prepared for sequencing using Takara ThruPLEX DNA-Seq Kit with Takara DNA Unique Dual Index Kit and paired-end sequenced at the UNC High Throughput Sequencing Facility with an Illumina Hi-Seq 4000.


title: DO-044_F_Islet

data_processing:
Assembly: GRCm38
Supplementary files format and content: DO_RNAseq_islet_counts_matrix.csv
Supplementary files format and content: DO_RNAseq_islet_mrna_annots.csv
Supplementary files format and content: DO_RNAseq_islet_vst_matrix.csv
Islet: processed DO islet RNAseq data (legacy data, reprocessed with batch effects removed as reported in /RNAseq/Raw/GBRS/QTLViewer_setup/QTLv_format_ISLET_REMOVE_BATCH.R script).
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.
counts_matrix.csv: raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.
vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
mrna_annots.csv: gene annotation file ENSEMBL version 75.
QTLViewer: QTLViewer data object and documentation. QTLViewer object generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.
GBRS_QTL2_genoprobs: final genoprobs on QTL2 format generated through GBRS for each tissue (used for genotype QCing). Genoprobs generated by the R script /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_genoprobs.R

value: pancreatic islet


title: DO-041_F_Islet


title: CON18_T1

value: vigorous


title: DO-040_F_Islet


title: Wing disc, HP1a-chromo, FAIREseq, rep1


title: Wing disc, HP1a-chromo, FAIREseq, rep2


title: CON18_T2

value: healthy control (CON)


title: Whole blood Animal PA70 at D105 after 68-1 CyCMV/flu vaccination

value: Non protected


title: Whole blood Animal PA63 at D105 after 68-1 CyCMV/flu vaccination


title: Wing disc, CrGFP-HP1chromo, GFP, rep1, sup

value: yw; CrGFP-HP1chromo/Cyo, Tb, RFP; +


title: CON17_T2

value: time 2

value: male


title: DO-039_F_Islet


title: Wing disc, HP1a-control, FAIREseq, rep3

value: wing disc


title: Whole blood Animal PA62 at D105 after 68-1 CyCMV/flu vaccination


title: Whole blood Animal PA77 at D105 after 68-1 CyCMV/flu vaccination


title: Wing disc, HP1a-control, FAIREseq, rep2


title: CON17_T1

value: time 1

value: moderate


title: Whole blood Animal PA75 at D14 after full length CyCMV/flu vaccination

value: full length CyCMV/flu


title: DO-038_F_Islet


title: CON14_T1


title: Wing disc, HP1a-control, FAIREseq, rep1


title: Whole blood Animal PA73 at D14 after full length CyCMV/flu vaccination

value: Deceased

value: Female


title: CON14_T2


title: DO-037_F_Islet


title: DO-036_F_Islet


title: CON13_T2


title: Wing disc, K9R, HP1a, rep2

data_processing:
Fastq files for biological replicates were combined. Adapters were trimmed using bbmap version 38.71 and parameters ktrim=k, ref=adapters, rcomp=t, tpe=t, tbo=t, hdist=1, mink=11 for all fastq files (individual replicates and merged fastq files). Trimmed reads were aligned to the dm6 reference genome using bowtie2 version 2.3.4.1 and parameters --seed 123 -q --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 400. Sam files were then converted to bam files and reads were filtered using samtools version 1.10 such that only reads with a MAPQ greater than 5 were kept. Bam files were sorted using samtools and converted to bed files using bedtools version 2.26. Read depth was calculated and rpgc-normalized bedgraphs were generated from bed files using bedtools. Bedgraphs were converted to bigWigs using ucsctools version 320. Peaks were called from bed files using macs2 version 2.1.2 with parameters --nomodel, --seed 123. As a control for peak calling, we used sonicated genomic DNA.
Peak calls from negative control experiments were used to create a list of blacklisted peaks for each experimental antibody, which were filtered out of experimental data using the bedtools function intersect with option -v at the bam to bed file conversion step. Peaks called from IgG CUT&RUN were used in blacklists for all experiments. Peak calls from additional negative control experiments were combined with IgG peak calls to create specific blacklists for each experiment, as follows. For C1A9 HP1a CUT&RUN, only IgG peaks were blacklisted. For GFP-HP1a CUT&RUN, peaks called from anti-GFP CUT&RUN on yw wing imaginal discs, which lack the GFP epitope, were combined with IgG peaks. For H3K9me3 CUT&RUN, we examined the possibility that loss of the H3K9me3 epitope in H3.2K9R wings resulted in cross-reactivity of the H3K9me3 antibody with H3K27me3 due to similarity in the surrounding amino acids80. Comparison of H3K9me3 and H3K27me3 signals in H3.2HWT and H3.2K9R CUT&RUN showed evidence of cross-reactivity (Figure S3F-G). Therefore, we included peaks called from H3K27me3 CUT&RUN in the blacklist for H3K9me3 CUT&RUN. H3.2HWT H3K27me3 was used to blacklist H3.2HWT H3K9me3, H3.2K9R H3K27me3 was used to blacklist H3.2K9R H3K9me3, and yw H3K27me3 was used to blacklist HP1acontrol and HP1achromo H3K9me3 profiles.
Assembly: dm6
Library strategy: CUT&RUN

value: HP1a (DSHB #C1A9)


title: DO-034_F_Islet


title: CON13_T1

value: Whole blood


title: Wing disc, K9R, HP1a, rep1


title: Whole blood Animal PA67 at D14 after full length CyCMV/flu vaccination

value: Whole Blood PAXgene


title: CON12_T2


title: Wing disc, K9R, HP1a, rep3


title: Whole blood Animal PA65 at D14 after full length CyCMV/flu vaccination

value: Protected

value: Male


title: Whole blood Animal PA64 at D14 after full length CyCMV/flu vaccination


title: Wing disc, HWT, HP1a, rep5

value: HWT


title: CON12_T1

value: healthy control (CON)

value: vigorous


title: DO-032_F_Islet

value: pancreatic islet

value: 45% fat


title: Wing disc, HWT, HP1a, rep4


title: Whole blood Animal PA77 at D14 after 68-1 CyCMV/flu vaccination

value: 68-1 CyCMV/flu


title: CON11_T2

value: time 2

value: female


title: Whole blood Animal PA72 at D14 after 68-1 CyCMV/flu vaccination


title: Wing disc, HWT, HP1a, rep3

value: wing disc


title: DO-031_F_Islet


title: Whole blood Animal PA69 at D14 after full length CyCMV/flu vaccination

value: full length CyCMV/flu


title: DO-035_F_Islet


title: DO-027_F_Islet


title: CON10_T2

value: moderate


title: Wing disc, HWT, HP1a, rep1


title: CON11_T1

value: time 1


title: DO-030_F_Islet


title: Whole blood Animal PA70 at D14 after 68-1 CyCMV/flu vaccination

value: Non protected


title: DO-026_F_Islet


title: Wing disc, HWT, HP1a, rep2

value: HP1a (DSHB #C1A9)


title: Wing disc, HP1a-chromo, HP1a, rep3


title: DO-033_F_Islet


title: Whole blood Animal PA63 at D14 after 68-1 CyCMV/flu vaccination

value: Whole Blood PAXgene


title: CON09_T2

value: Whole blood

value: male


title: CON10_T1


title: Wing disc, HP1a-chromo, HP1a, rep2


title: CON09_T1


title: DO-025_F_Islet


title: Wing disc, HP1a-chromo, HP1a, rep1


title: Whole blood Animal PA62 at D14 after 68-1 CyCMV/flu vaccination

value: Protected

value: Male


title: CON08_T2

value: healthy control (CON)


title: DO-024_F_Islet

value: pancreatic islet


title: Whole blood Animal PA75 at D3 after full length CyCMV/flu vaccination

value: Day 3


title: Wing disc, HP1a-control, HP1a, rep5


title: DO-023_F_Islet

value: 45% fat


title: Whole blood Animal PA73 at D3 after full length CyCMV/flu vaccination

value: Deceased

value: Female


title: DO-022_F_Islet


title: Wing disc, HP1a-control, HP1a, rep4

value: wing disc


title: CON08_T1


title: Whole blood Animal PA71 at D14 after 68-1 CyCMV/flu vaccination

value: 68-1 CyCMV/flu


title: CON07_T2

value: time 2

value: moderate


title: Whole blood Animal PA69 at D3 after full length CyCMV/flu vaccination

value: full length CyCMV/flu


title: Wing disc, HP1a-control, HP1a, rep3

value: HP1a (DSHB #C1A9)


title: Wt-2

city: Baltimore

first: Emmanouil

last: Tampakakis

state: Maryland

address: 720 Rutland Ave, Ross 1033

department: Division of Cardiology

institute: Johns Hopkins School of Medicine

data_processing:
Raw sequencing reads were trimmed using Trimmomatic (0.36) with a minimum quality threshold of 35 and minimum length of 3624.
Processed reads were mapped to the mm10 reference genome using HISAT2
Counts were then assembled using Subread featureCounts
Differential gene expression analysis was done using the DESeq2 package in R.
Assembly: mm10
Supplementary files format and content: csv raw counts table, gene names as row names and sample name as column names

source_name: Heart

extract_protocol:
Hearts from the same mouse liter at P40 were harvested, and homogenized in Trizol (Thermo Fisher) and RNA was isolated following the manufacturer’s instructions
cDNA libraries for bulk-RNA sequencing were prepared using the TruSeq kit (Illumina) and sequenced using HiSeq 2500 at the Johns Hopkins University Sequencing Core

value: Heart

value: adult; P40

value: WT


title: Wt-1


title: CON07_T1

value: Whole blood

value: time 1

value: male


title: CON06_T2

value: healthy control (CON)

value: vigorous

value: female


title: Whole blood Animal PA64 at D3 after full length CyCMV/flu vaccination

value: Day 3

value: Non protected

value: Male

value: Whole Blood PAXgene


title: Wing disc, HP1a-control, HP1a, rep1

value: wing disc


title: Whole blood Animal PA65 at D3 after full length CyCMV/flu vaccination

value: Protected


title: Wing disc, yw, GFP, rep2, pel


title: CON06_T1


title: Homo-3

value: homozygotes mice with enhancer deletion


title: Homo-2


title: Wing disc, yw, GFP, rep1, pel


title: CON05_T2

value: time 2

value: moderate


title: CON05_T1


title: Whole blood Animal PA72 at D3 after 68-1 CyCMV/flu vaccination

value: Female

value: 68-1 CyCMV/flu


title: Homo-1

value: Heart

value: adult; P40


title: Wing disc, GFP-HP1a/+, GFP, rep1, pel


title: CON02_T2

value: Whole blood

value: male


title: Whole blood Animal PA71 at D3 after 68-1 CyCMV/flu vaccination


title: Wing disc, GFP-HP1a/+, GFP, rep1, sup


title: Whole blood Animal PA67 at D3 after full length CyCMV/flu vaccination

value: full length CyCMV/flu


title: CON02_T1

value: healthy control (CON)

value: time 1


title: DO-021_F_Islet

value: pancreatic islet

value: 45% fat


title: Het-3

value: heterozygotes with enhancer deletion


title: Het-2


title: Wing disc, GFP-HP1a/GFP-HP1a, GFP, rep2, pel

value: wing disc


title: Whole blood Animal PA70 at D3 after 68-1 CyCMV/flu vaccination

value: Day 3

value: Non protected

value: Male

value: Whole Blood PAXgene


title: Wing disc, HP1a-control, HP1a, rep2

value: HP1a (DSHB #C1A9)


title: Whole blood Animal PA63 at D3 after 68-1 CyCMV/flu vaccination

value: 68-1 CyCMV/flu


title: Wing disc, GFP-HP1a/GFP-HP1a, GFP, rep2, sup


title: Whole blood Animal PA77 at D3 after 68-1 CyCMV/flu vaccination

value: Protected


title: Wing disc, GFP-HP1a/GFP-HP1a, GFP, rep1, pel


title: L_NOD8

city: Lausanne

first: Flora

last: Brozzi

address: Rue du Bugnon 9

department: DNF

country: Switzerland

institute: University of Lausanne

description: Read Count L

data_processing:
3' adapter (AACTGTAGGCACCATCAAT) trimmed and identical reads collapsed based on Unique Molecular Indentifier (UMI)
perfectly mapped to tRNAs using bowtie (version 1)
To investigate the expression profiles of tRNA fragments, the frequency of tRF counts were normalized to TPM using the following formula: normalized expression = actual tRF read count / total clean read count × 1000000.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include tRF TPM values for each sample

source_name: Islets of Langerhans

growth_protocol: Islets from female NOD/ShiLtJ (aged 4 and 8 weeks) mice were isolated as follow. Mouse pancreases were digested with collagenase (Sigma), and islets isolated by Histopaque (Sigma) density gradient and handpicking. Purified islet cells were cultured in RPMI 1640 GlutaMAX medium (ThermoFisher) supplemented with 10% FCS, 100 U/mL penicillin and 100 µg/mL streptomycin, 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma), and left in culture overnight before RNA extraction.

extract_protocol:
RNA was extracted with miRNeasy kit (Qiagen), and prior to library preparation, RNA was pretreated with rtStar™ tRF&tiRNA Pretreatment Kit (AS-FS-005, Arraystar)
Libraries were prepared with QIAseq miRNA Library Kit (Qiagen) following manufacter's protocol.

value: Islets of Langerhans

tag: cell type

value: Beta-cells and alpha-cells mainly

value: NOD/ShiLtJ

value: Overnight culture


title: Whole blood Animal PA62 at D3 after 68-1 CyCMV/flu vaccination


title: K_NOD8

description: Read Count K

tag: genotype


title: Wing disc, GFP-HP1a/GFP-HP1a, GFP, rep1, sup


title: hESC.rep2

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Gene expression level was calculated using EDASeq (v2.4.1)
Assembly: hg38

source_name: neonatal skin fibroblasts

growth_protocol: hESCs were routinely cultured in mTeSRTM1 medium (STEMCELL Technologies, 85850)

extract_protocol:
TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: routinely cultured without special treatment

value: skin fibroblasts

tag: cell line

value: BJ

value: wild type

value: NO Treatment

tag: passage


title: hESC.SG_KI.rep1

value: C-SSX koncked in SS18 locus


title: hESC.rep1


title: I_NOD8

description: Read Count I


title: Wing disc, K9R, H3K27me3, rep3

value: wing disc


title: Whole blood Animal PA69 at D0 before full length CyCMV/flu

tag: time point

value: Day 0

tag: vaccination outcome

tag: animall id

value: full length CyCMV/flu


title: Wing disc, K9R, H3K27me3, rep2


title: H_NOD8

description: Read Count H

tag: treatment


title: SS

description: HiC data

data_processing:
Hi-C datasets were processed using HiC-Pro (Version 3.1.0) with GATCGATC(MboI) ligation site. The duplicate reads and the invalid interactions were removed.
hicpro2juicebox tool to generate Juicebox-compatible files and Juicer tools software (Version 1.22.01) was used for visualization.
Assembly: hg38

growth_protocol: BJ fibroblasts were cultured by 10% FBS medium (DMEM, 10%FBS, NEAA, GlutaMAX)

extract_protocol:
Crosslink 1 million cells with 37% formaldehyde(sigma, F8775) to a final concentration of 1% and incubate for 10 min at room temperature. Add glycine(Yuanye, S20159) to a final concentration of 0.125M, and terminate the formaldehyde crosslinking reaction at room temperature for 5 min. Cells were pelleted by spinning at 400g for 5 min at 4°C. The pellet was washed with cold PBS. Liquid nitrogen quick-freeze, placed at -80 degrees for reserve.fixed cells were incubated in 500μl of cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% Igepal CA630 and protease inhibitors (MCE-HY-K0010)) on ice for 25 min. Cells were pelleted by spinning at 400g for 5 min at 4°C. The pellet was washed twice with 1xNEBuffer2. Cells were resuspended in 50μl of 0.5%SDS and incubated for 8 min at 62°C. Next, reactions were terminated with 145μl of water and 25μl of 10%Triton X-100 (Sigma, 93443) at 37°C for 15min. Sample was digested overnight with 25μl of 10X NEBuffer2 and 20μl of MboI(NEB, R0147, 5U/µl) at 37 °C with rotation. Incubate the reactants at 62°C for 20min to inactivate MboI, then cold to room temperature.To complement the bases at the sticky end and label biotin at the DNA end, add 50μl of the mixture（37.5μl 0.4 mM biotin-14-dATP, 1.5μl of 10mMdCTP, 1.5μl of 10mM dGTP, 1.5μlof 10mM dTTP, and 8μl of 5U/μl DNA polymerase I, large (Klenow) fragment(NEB M0210)）and incubating at 37°C for 4h. After that, ligation is performed by adding 120μl of 10XNEB T4 DNA ligase buffer(NEB,B0202L), 100μl of 10% Triton X-100, 637.8μl of water, 1.2μl of 10%BSA(Sigma-Aldrich SRE0098) and 5μl of 400 U/μl T4 DNA ligase(NEB,M0202L) and incubating for 6h at room temperature. De-crosslinking was performed by adding 50μL of 20mg/mL proteinase K (NEB, P8107) and 120μL of 10%SDS incubate at 55°C for 30min. And then 130μL of 5M NaCl was added and incubated at 68 °C overnight. Samples were cooled to room temperature and divided into three equal portions. Then, 800μl of pure ethanol and 50μl of 3M sodium acetate pH5.2 were added to each tube which were subsequently incubated for 30 min at -80°C. Spin the tubes at maximum speed for 15 min at 4°C and wash twice with 70% ethanol. Resuspend the resulting pellet in 130μl of 10mM Tris-HCl, pH8.0 and incubate at 37 °C for 15 min.DNA was sheared using an ME220 Covaris Focused-ultrasonicator to a fragment size of 300–500 bp. Sheared DNA was size selected using VAHTS® DNA Clean Beads N411. Elution was done with hot (65°C) 70μl EB buffer. Next, the sample is transferred to a DNA LoBind tube (Eppendorf, 30108418) for related experimental manipulation. Take 150ul of T1 beads (MyOne Streptavin T1 Beads, Invitrogen, 65601) into a DNA LoBind Tubes and add 500ul 1x TWB buffer (5mM Tris-HCl (pH 7.5); 0.5mM EDTA; 1M NaCl; 0.05% Tween 20) wash twice. Resuspend the T1 beads with 70ul 2× Binding Buffer (10mM Tris-HCl (pH 7.5), 1mM EDTA, 2M NaCl) and combined with 70μl Hi-C DNA from the previous step. The mixture was incubated at room temperature for 15min . After which the magnet adsorbed to remove the supernatant; Wash twice with 200ul 1x TWB buffer and once with 200ul EB buffer. Finally, resuspend the beads with 50ul of water and transfer to a 200ul PCR tube.
Library construction using the VAHTS Universal DNA Library Prep Kit (Vazyme ND607) and VAHTS Multiplex Oligos Set 4/5 kits (Vazyme N321/N322) according to manufacturer’s instructions

tag: passages

value: SS18-SSX1 overexpression


title: Whole blood Animal PA65 at D0 before full length CyCMV/flu

value: Male

value: Whole Blood PAXgene


title: hESC.SG_KI.rep2


title: Whole blood Animal PA67 at D0 before  full length CyCMV/flu

value: Non protected


title: G_NOD4

description: Read Count G


title: Wing disc, K9R, H3K27me3, rep1


title: MUT

description: HiC data

value: SS18(YA)-SSX1 mutant overexpression


title: Whole blood Animal PA75 at D0 before full length CyCMV/flu


title: Het-1

value: Heart

value: adult; P40

value: heterozygotes with enhancer deletion


title: Wing disc, HWT, H3K27me3, rep2

value: HWT


title: SS18

description: HiC data

value: skin fibroblasts

value: EGFP overexpression


title: F_NOD4

description: Read Count F

value: Islets of Langerhans

value: Beta-cells and alpha-cells mainly

value: NOD/ShiLtJ

value: Overnight culture


title: SS-HA

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Assembly: hg38

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions

value: BJ

value: wild type

tag: chip antibody

value: CST no 3724S

value: SS18-SSX1-HA overexpression


title: Whole blood Animal PA64 at D0 before full length CyCMV/flu

value: Day 0

value: Male

value: Whole Blood PAXgene

value: full length CyCMV/flu


title: Whole blood Animal PA73 at D0 before full length CyCMV/flu

value: Deceased

value: Female


title: SS(YA)-HA

value: SS18(YA)-SSX1-HA overexpression


title: E_NOD4

description: Read Count E


title: Cyt4

description: Read Count Cyt4

library_source: other

molecule: other

growth_protocol: Mouse pancreases from C57BL/6NRj mice were digested with collagenase (Sigma), and islets isolated by Histopaque (Sigma) density gradient and handpicking. Purified islet cells were cultured in RPMI 1640 GlutaMAX medium (ThermoFisher) supplemented with 10% FCS, 100 U/mL penicillin and 100 µg/mL streptomycin, 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma). Rodent islets were dissociated into single cells by incubation in Ca2+/Mg2+free phosphate-buffered saline, 3 mM EGTA, and 0.002% trypsin (ThermoFisher) for 2-3 min at 37 °C and cultured 24h before treatment.

treatment_protocol: Dissociated islet cells were treated for 24 h, with a mix of the pro-inflammatory cytokines (PeproTech) IL-1β (0.1 ng/mL), TNF-α (10 ng/mL), and IFN-γ (30 ng/mL)

value: C57BL/6NRj mice

value: Cytokine mix


title: Whole blood Animal PA72 at D0 before 68-1 CyCMV/flu vaccination

value: Protected

value: 68-1 CyCMV/flu


title: SS-endo_SS18

value: skin fibroblasts

value: CST no 21792S

value: SS18-SSX1(epitope mutation of endo_SS18 antibody) overexpression


title: Wing disc, yw, H3K9me3, rep3

value: wing disc

value: H3K9me3 (Abcam #ab8898)

value: yw


title: Whole blood Animal PA71 at D0 before 68-1 CyCMV/flu vaccination

value: Day 0


title: EGFP-endo_SS18

value: BJ

value: wild type

value: EGFP overexpression


title: Cyt2

description: Read Count Cyt2

value: Islets of Langerhans

value: Beta-cells and alpha-cells mainly


title: Wing disc, yw, H3K9me3, rep2


title: Whole blood Animal PA70 at D0 before 68-1 CyCMV/flu vaccination

value: Non protected

value: Male

value: Whole Blood PAXgene


title: CTL rep 3

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 3

data_processing:
Trimmed for adapter sequences using Trimmomatic-0.36 to trim overrepresented sequences.
Alignment and annotated the raw data to the Homo sapiens NCBI GRCh38 genome using HISAT2.
Assemble the mapped reads into possible transcripts and generate a transcriptome assembly with Cufflinks.
Calculation of counts with HTSeq.
Variance stabilization performed using log2 scaling.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include log2 counts values for each sample

source_name: CTL rep 3

growth_protocol: Healthy human donor’s bone marrow mesenchymal stromal cells (hBM-MSCs) we obtained from different commercial providers (Lonza, Cat.# PT-2501, Cambrex, Cat.# PT-2501, Millipore, Cat.# SCR108, Inbiobank, Cat.# hMSC). All donor cells were obtained under informed consent and tested for the absence of endothelial and hematopoietic markers, presence of specific mesenchymal markers and their ability to differentiate to osteogenic, chondrogenic and adipogenic phenotype, as defined by ISCT (the International Society for Cellular Therapy) criteria. Cells were expanded in MSCBM mesenchymal cell basal medium (Stem Cells Tech, Cat.# 5401) supplemented with 10% Fetal bovine Serum (FBS) (Gibco, Cat.# 10500064) and antibiotics (Gibco, Cat.# 15140122). Subcultures were performed when cells arrived at 80% confluence by conventional enzymatic cell detachment with trypsin-EDTA 0,25% (Gibco, Cat.# 25200056), followed by cell counting and seeding at 6000 cells/cm2 for subculture, or 100000 cells/well in 6-well plates (Corning, Cat.# 3516) for differentiation assays.

extract_protocol:
Briefly, Gelfoam gelatin sponges (Pfizer, Cat.# 0009-0323-01) were sectioned into 48 pieces, washed with ethanol 70% (Scharlab, Cat.# ET0003005P) and rehydrated in sterile PBS (Gibco, Cat.# 14040). hBM-MSCs were diluted in culture media at 1x106 cells/ml and 100microl (1x105 cells) were carefully inoculated in each scaffold using a 1mL syringe (Braun, Cat.# 9161406V) with 25G needle (Braun, Cat.# 9186166).  Cell-seeded scaffolds were transferred to polystyrene ultra-low attachment 24 well plates (Corning, Cat.# 3473) and maintained in cell culture conditions for 3-5 hours. Then, culture media was added and scaffolds were cultured for 3 to 7 days. 5 microL of acetic acid (Fluka, Cat.# 27225) 50 mM reconstituted rhBMP-2 (Noricum, Cat.# rhBMP-2) (concentration at 5 microg/microL) were added. Then, 30 microL of 2% CaCl2 reconstituted thrombin from human plasma (Merck, Cat.# T8885) and 30 microL of water reconstituted fibrinogen from human plasma (Merck, Cat.# F3879) were incorporated.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: rhBMP-2 and hBM-MSC carrier implants were prepared as previously described.

value: CTL


title: Wing disc, HWT, H3K27me3, rep3

value: HWT


title: Whole blood Animal PA63 at D0 before 68-1 CyCMV/flu vaccination

value: 68-1 CyCMV/flu


title: Wing disc, yw, H3K9me3, rep1


title: CTL rep 2

description: replicate 2

source_name: CTL rep 2

value: bone marrow mesenchymal stromal cells (hBM-MSCs)


title: C4

description: Read Count C4

value: C57BL/6NRj mice

value: Control


title: Wing disc, K9R, H3K9me3, rep3

value: wing disc

value: H3K9me3 (Abcam #ab8898)


title: Whole blood Animal PA77 at D0 before 68-1 CyCMV/flu vaccination

value: Day 0

value: Protected


title: Whole blood Animal PA62 at D0 before 68-1 CyCMV/flu vaccination


title: Wing disc, K9R, H3K9me3, rep2


title: C2

description: Read Count C2


title: C3

description: Read Count C3


title: CTL rep 1

description: replicate 1

source_name: CTL rep 1


title: Wing disc, HWT, H3K27me3, rep1


title: Wing disc, K9R, H3K9me3, rep1


title: Whole blood Animal PA75 at baseline (2wks) before full length CyCMV/flu vaccination

value: Baseline

value: full length CyCMV/flu


title: BMP2 rep 3

description: replicate 3

source_name: BMP2 rep 3


title: Cyt3

description: Read Count Cyt3

value: Islets of Langerhans

value: Cytokine mix


title: BMP2 rep 2

description: replicate 2

source_name: BMP2 rep 2


title: Whole blood Animal PA73 at baseline (2wks) before full length CyCMV/flu vaccination

value: Deceased

value: Female


title: Wing disc, HWT, H3K9me3, rep3


title: Whole blood Animal PA69 at baseline (2wks) before full length CyCMV/flu vaccination

value: Male

value: Whole Blood PAXgene


title: Wing disc, HWT, H3K9me3, rep2

value: HWT


title: C1

description: Read Count C1

value: Beta-cells and alpha-cells mainly


title: Whole blood Animal PA67 at baseline (2wks) before full length CyCMV/flu vaccination

value: Non protected


title: neonatal skin fibroblasts, SS-A485-rep3

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Gene expression level was calculated using EDASeq (v2.4.1)
Assembly: hg38
Supplementary files format and content: Comma-separated value file containing  counts data

treatment_protocol: Treated with 1µM A485

value: skin fibroblasts

value: BJ

value: wild type

value: SS18-SSX1 overexpression with treatment by A485


title: EN1B

description: Read Count EN1B

data_processing:
3' adapter (AACTGTAGGCACCATCAAT) trimmed and identical reads collapsed based on Unique Molecular Indentifier (UMI)
perfectly mapped to tRNAs using bowtie (version 1)
To investigate the expression profiles of tRNA fragments, the frequency of tRF counts were normalized to TPM using the following formula: normalized expression = actual tRF read count / total clean read count × 1000000.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited xlsx file include tRF TPM values for each sample

source_name: lymphoid tissues

growth_protocol: Mouse CD4+/CD25- T-cells were purified from lymphoid tissues of NOD/ShiLtJ mice, using CD4+CD25+ Regulatory T Cell Isolation Kit (Miltenyi Biotec). After isolation, murine CD4+/CD25– T cells were incubated in RPMI 1640-medium supplemented with 10% EV-free depleted FCS, 100 μg/mL streptomycin and 100 IU/mL penicillin and were stimulated for 72 hr with 20 ng/mL IL-12 and 200 UI/mL IL-2 (R&D system Europe) and CD3/CD28 Abs (InvitrogenThermoFisher). After 3 days, media was collected for EV isolation and RNA extraction. EVs were isolated by ultra-centrifugation as previously described (Guay C, 2019). Briefly, the culture media of primary T cells was collected and centrifuged first at 300 x g for 6 min to pellet cells and then at 2,000 x g for 10 min to discard dead cells. Supernatants were centrifuged at 10,000 x g for 30 min to remove cell debris. EVs were then isolated from the supernatant by ultracentrifugation at 100,000 x g for 2 hr. The pellet containing the EVs was washed twice with PBS and re-centrifuged at 100’000 x g for 2h. EVs were collected in Qiazol for small RNA extraction.

value: lymphoid tissues

value: CD4+/ CD25- T-cells

tag: cellular part

value: Extracellular Vesicles

value: NOD/ShiLtJ

value: Activation with CD3/CD28 Abs


title: Cyt1

description: Read Count Cyt1

value: Islets of Langerhans

tag: age

value: C57BL/6NRj mice

value: Cytokine mix


title: Wing disc, HWT, H3K9me3, rep1

value: wing disc

value: H3K9me3 (Abcam #ab8898)


title: Whole blood Animal PA65 at baseline (2wks) before full length CyCMV/flu vaccination

value: Baseline

value: Protected

value: Male

value: Whole Blood PAXgene

value: full length CyCMV/flu


title: Whole blood Animal PA64 at baseline (2wks) before full length CyCMV/flu vaccination

value: Non protected


title: EN1A

description: Read Count EN1A


title: F11

description: Read Count F11

treatment_protocol: Dispersed islet cells were incubated with EV produced by CD4+/CD25- T-cells, isolated from  NOD/ShiLtJ mice. The number of EVs added to the recipient cells was estimated using Zetasizer Ultra (Malvern Panalytical), measuring both particle size and concentration. The recipient cells were exposed to EV concentrations of about 1x1011/mL These concentrations are within the same range of those reported in murine and human plasma samples (Matsumoto et al., 2016, Thomou et al., 2017). RNA was collected after 24h of EV-treatment.

value: Beta-cells and alpha-cells mainly

value: Evs


title: Wing disc, HP1a-chromo, H3K9me3, rep3


title: neonatal skin fibroblasts, SS-A485-rep2

value: skin fibroblasts

value: BJ

value: wild type

value: SS18-SSX1 overexpression with treatment by A485


title: neonatal skin fibroblasts, SS-A485-rep1


title: Wing disc, HP1a-chromo, H3K9me3, rep2


title: Whole blood Animal PA77 at baseline (2wks) before 68-1 CyCMV/flu vaccination

value: 68-1 CyCMV/flu


title: neonatal skin fibroblasts, SS-rep3

value: SS18-SSX1 overexpression


title: F10

description: Read Count F10

value: Islets of Langerhans

value: C57BL/6NRj mice

value: Control


title: BMP2 rep 1

description: replicate 1

source_name: BMP2 rep 1

value: bone marrow mesenchymal stromal cells (hBM-MSCs)


title: Whole blood Animal PA71 at baseline (2wks) before 68-1 CyCMV/flu vaccination

value: Baseline

value: Protected


title: Wing disc, HP1a-chromo, H3K9me3, rep1

value: wing disc

value: H3K9me3 (Abcam #ab8898)


title: F8

description: Read Count F8


title: neonatal skin fibroblasts, SS-rep2


title: EN2A

description: Read Count EN2A

value: lymphoid tissues

value: CD4+/ CD25- T-cells

value: Extracellular Vesicles

value: NOD/ShiLtJ

value: Activation with CD3/CD28 Abs


title: Whole blood Animal PA72 at baseline (2wks) before 68-1 CyCMV/flu vaccination

value: Female

value: Whole Blood PAXgene


title: Wing disc, HP1a-control, H3K9me3, rep2


title: neonatal skin fibroblasts, WT-rep3

value: skin fibroblasts

value: BJ

value: wild type

value: EGFP overexpression


title: Wing disc, HP1a-control, H3K9me3, rep3


title: F5

description: Read Count F5

value: Islets of Langerhans

value: Beta-cells and alpha-cells mainly

value: C57BL/6NRj mice

value: Evs


title: Whole blood Animal PA63 at baseline (2wks) before 68-1 CyCMV/flu vaccination

value: Baseline

value: Non protected

value: Male

value: 68-1 CyCMV/flu


title: Wing disc, HP1a-control, H3K9me3, rep1

value: wing disc

value: H3K9me3 (Abcam #ab8898)


title: F4

description: Read Count F4

value: Control


title: neonatal skin fibroblasts, WT-rep2


title: Whole blood Animal PA62 at baseline (2wks) before 68-1 CyCMV/flu vaccination

value: Protected


title: Setd1a KO-Metastatic cell  [RNA_seq_3_1350]

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
The RNA-seq datasets were processed using the RNA-seq pipeline implemented in snakePipe (Bhardwaj et al. 2019).
Specifically, paired-end reads were mapped to the mouse genome (mm10) using STAR aligner (Dobin et al. 2013) with default settings.
Reads mapped to genes were counted using featureCounts (Liao et al. 2014) to obtain the gene-level counts, and differential expression was done using DESeq in R (Love et al. 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample by featureCounts, text file

source_name: Setd1a KO-Metastatic cell

growth_protocol: mouse UPS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Direct-zol RNA mini prep kit (ZYMO RESEARCH). Total RNA ≥200ng, Concentration ≥20ng/μl of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for RNA sequencing using standard BGI protocols.

value: mouse Undifferentiated Pleomorphic Sarcoma (UPS) cell

value: Sarcoma cell line

value: Setd1a Knock Out


title: neonatal skin fibroblasts, WT-rep1

value: skin fibroblasts

value: BJ

value: wild type


title: neonatal skin fibroblasts, SS-SS18_SSX1

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Assembly: hg38
Supplementary files format and content: bigwig

treatment_protocol: SS18-SSX1 overexpression by lentiviral infection.

value: CST no 72364S

value: SS18-SSX1 overexpression


title: F1

description: Read Count F1

value: Islets of Langerhans

value: Beta-cells and alpha-cells mainly

value: C57BL/6NRj mice


title: Wing disc, K9R, HiC, rep2

description: Sequenced PEx150

data_processing:
These data were merged, aligned, filtered, and balanced by juicer. Only reads with MAPQ > 30 were kept.
Assembly: dm6
Supplementary files format and content: juicer
Supplementary files format and content: peakfile

extract_protocol:
Each in situ Hi-C replicate was performed using 60 wing imaginal discs dissected from female H3.2HWT, H3.2K9R, HP1-chromo, and HP1-control wandering L3 larvae. Discs were fixed in 1xPBS with 4% paraformaldehyde for 20min, transferred to tubes in a minimal volume of 1xPBS plus 0.15% Triton X-100, and used as input for the Arima Hi-C kit v00 protocol (A410030), following manufacturer’s instructions that were last revised March 2018.
Hi-C libraries were amplified using the KAPA Hyper Prep kit (KK8502).

tag: developmental stage


title: F2

description: Read Count F2

value: Evs


title: Wing disc, K9R, HiC, rep1

description: Sequenced PEx150


title: neonatal skin fibroblasts, SS-rep1


title: Setd1a KO-Metastatic cell  [RNA_seq_2_1350]


title: Whole blood Animal PA70 at baseline (2wks) before 68-1 CyCMV/flu vaccination

data_processing:
Sequenced reads were trimmed with Trim galore using default parameters version 0.6.4
Globin and rRNA reads filtered out with bowtie2 version 2.4.2
Reads aligned and quantified using STAR v 2.7.5 to rhesus macaque genome version10 with ensembl annotation version 100
Assembly: rhesus macaque genome version10 with ensembl annotation version 100
Supplementary files format and content: count_matrix.txt

value: Baseline

value: Non protected

value: Male

value: Whole Blood PAXgene

value: 68-1 CyCMV/flu


title: neonatal skin fibroblasts, ctr-SS18

value: CST no 21792S

value: EGFP overexpression


title: Wing disc, HWT, HiC, rep2

description: Sequenced PEx150

value: HWT

value: wing disc


title: F7

description: Read Count F7

value: Control


title: Wing disc, HWT, HiC, rep1

description: Sequenced PEx150


title: 26C_48h_3

city: cincinnati

first: XUEZHAO

last: LIU

institute: cincinnati children's hospital medical center

data_processing:
All RNA-seq data were aligned to mm9 or Rn5 using TopHat with default settings (http://tophat.cbcb.umd.edu/). We used Cuff-diff to (i) estimate fragments per kilobase of transcript per million mapped read (FPKM) values for known transcripts and to (ii) analyze differentially expressed transcripts. In all differential expression tests, a difference was considered significant if the p value was less than 0.05.
Assembly: mm10/rn5
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

value: brain

value: primary iOLs

value: oligodendrocytes

value: wildtype


title: Setd1a KO-Metastatic cell  [RNA_seq_1_1350]

value: mouse Undifferentiated Pleomorphic Sarcoma (UPS) cell

value: Sarcoma cell line

value: Setd1a Knock Out


title: neonatal skin fibroblasts, ctr-H3K27ac

value: skin fibroblasts

value: BJ

value: wild type

value: Abcam, ab4729


title: neonatal skin fibroblasts, SS-H3K27ac

value: SS18-SSX1 overexpression


title: Control-Metastatic cell  [RNA_seq_3_AAV2]

source_name: Control-Metastatic cell

value: WT


title: Wing disc, HP1a-chromo, HiC, rep1

description: Sequenced PEx150


title: Control-Metastatic cell  [RNA_seq_2_AAV2]


title: 26C_48h_2


title: Wing disc, HP1a-control, HiC, rep2

description: Sequenced PEx150


title: Wing disc, HP1a-chromo, HiC, rep2

description: Sequenced PEx150


title: veh1

value: DMSO


title: veh2


title: Wing disc, HP1a-control, HiC, rep1

description: Sequenced PEx150


title: Control-Metastatic cell  [RNA_seq_1_AAV2]


title: neonatal skin fibroblasts, SS-H2AK119ub

value: CST no 8240s